Résumé : We developed and characterized microsatellite markers for the genus Lotus, a large genus of leguminous plants containing many endemic species of conservation interest. The marker system was then used to survey patterns of population genetic variation of Lotus sessilifolius, a Canary Island endemic occurring on four islands (La Palma, El Hierro, La Gomera and Tenerife) with the aim of determining whether any of its populations are worthy of special conservation because of genetic distinctiveness. We found strong differentiation between populations with conspicuous geographical signal revealed by population clustering. Generally, populations from each island grouped together. A very striking exception to this pattern is a single population from Tenerife (Tejina-Milán: Anaga Peninsula), which is separated from other Tenerife populations by both genetic clustering and a STRUCTURE analysis, and also shows signs of inbreeding. The genetic distinctiveness of this population deserves especial conservation attention, and may be related to the ancient geological history of the Anaga Peninsula. Importantly, this investigation sets the stage for conservation genetics research in other highly threatened species in the same genus.